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- EMDB-14312: phospho-STING binding to adaptor protein complex-1 -

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Basic information

Entry
Database: EMDB / ID: EMD-14312
Titlephospho-STING binding to adaptor protein complex-1
Map data
Sample
  • Complex: phospho-STING binding to adaptor protein complex-1
    • Protein or peptide: AP-1 complex subunit beta-1AP-1 transcription factor
    • Protein or peptide: ADP-ribosylation factor 1ARF1
    • Protein or peptide: AP-1 complex subunit gamma-1AP-1 transcription factor
    • Protein or peptide: Stimulator of interferon genes protein
    • Protein or peptide: AP-1 complex subunit mu-1AP-1 transcription factor
    • Protein or peptide: AP-1 complex subunit sigma-3AP-1 transcription factor
  • Ligand: GUANOSINE-5'-TRIPHOSPHATEGuanosine triphosphate
  • Ligand: MAGNESIUM ION
Function / homology
Function and homology information


basolateral protein secretion / mitotic cleavage furrow ingression / AP-1 adaptor complex / trans-Golgi Network Vesicle Budding / endosome to melanosome transport / positive regulation of natural killer cell degranulation / Lysosome Vesicle Biogenesis / platelet dense granule organization / regulation of receptor internalization / melanosome assembly ...basolateral protein secretion / mitotic cleavage furrow ingression / AP-1 adaptor complex / trans-Golgi Network Vesicle Budding / endosome to melanosome transport / positive regulation of natural killer cell degranulation / Lysosome Vesicle Biogenesis / platelet dense granule organization / regulation of receptor internalization / melanosome assembly / regulation of Arp2/3 complex-mediated actin nucleation / STING complex / Golgi to lysosome transport / Intra-Golgi traffic / Golgi to vacuole transport / STAT6-mediated induction of chemokines / Synthesis of PIPs at the Golgi membrane / Golgi Associated Vesicle Biogenesis / serine/threonine protein kinase complex / 2',3'-cyclic GMP-AMP binding / proton channel activity / GTP-dependent protein binding / clathrin adaptor activity / cyclic-di-GMP binding / STING mediated induction of host immune responses / MHC class II antigen presentation / melanosome organization / Nef Mediated CD4 Down-regulation / IRF3-mediated induction of type I IFN / cGAS/STING signaling pathway / dendritic spine organization / positive regulation of type I interferon-mediated signaling pathway / reticulophagy / determination of left/right symmetry / long-term synaptic depression / COPI-dependent Golgi-to-ER retrograde traffic / clathrin-coated vesicle / Lysosome Vesicle Biogenesis / pattern recognition receptor signaling pathway / clathrin binding / Golgi Associated Vesicle Biogenesis / positive regulation of natural killer cell mediated cytotoxicity / cellular response to exogenous dsRNA / cytoplasmic pattern recognition receptor signaling pathway / cell leading edge / autophagosome membrane / Synthesis of PIPs at the plasma membrane / antiviral innate immune response / positive regulation of macroautophagy / kinesin binding / autophagosome assembly / intracellular copper ion homeostasis / cellular response to organic cyclic compound / autophagosome / protein targeting / positive regulation of type I interferon production / cellular response to interferon-beta / signaling adaptor activity / COPI-mediated anterograde transport / clathrin-coated pit / vesicle-mediated transport / positive regulation of defense response to virus by host / MHC class II antigen presentation / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / Regulation of innate immune responses to cytosolic DNA / activation of innate immune response / endoplasmic reticulum-Golgi intermediate compartment membrane / Neutrophil degranulation / positive regulation of interferon-beta production / sarcomere / small monomeric GTPase / secretory granule membrane / trans-Golgi network membrane / Nef mediated downregulation of MHC class I complex cell surface expression / kidney development / intracellular protein transport / cytoplasmic vesicle membrane / trans-Golgi network / recycling endosome / cellular response to virus / small GTPase binding / peroxisome / SARS-CoV-1 activates/modulates innate immune responses / positive regulation of DNA-binding transcription factor activity / protein complex oligomerization / heart development / positive regulation of protein binding / regulation of inflammatory response / defense response to virus / mitochondrial outer membrane / RNA polymerase II-specific DNA-binding transcription factor binding / postsynaptic density / early endosome / endosome / neuron projection / lysosomal membrane / protein domain specific binding / Golgi membrane / focal adhesion / intracellular membrane-bounded organelle
Similarity search - Function
AP-1 complex subunit sigma / Adaptor protein complex AP-1, gamma subunit / Gamma-adaptin ear (GAE) domain / Gamma-adaptin ear (GAE) domain profile. / ADP-ribosylation factor 1-5 / Adaptor protein complex, sigma subunit / Clathrin adaptor, beta-adaptin, appendage, Ig-like subdomain / Beta-adaptin appendage, C-terminal subdomain / AP-1/2/4 complex subunit beta / Beta2-adaptin appendage, C-terminal sub-domain ...AP-1 complex subunit sigma / Adaptor protein complex AP-1, gamma subunit / Gamma-adaptin ear (GAE) domain / Gamma-adaptin ear (GAE) domain profile. / ADP-ribosylation factor 1-5 / Adaptor protein complex, sigma subunit / Clathrin adaptor, beta-adaptin, appendage, Ig-like subdomain / Beta-adaptin appendage, C-terminal subdomain / AP-1/2/4 complex subunit beta / Beta2-adaptin appendage, C-terminal sub-domain / Beta2-adaptin appendage, C-terminal sub-domain / AP complex subunit beta / Clathrin adaptor complex, small chain / Clathrin adaptor complexes small chain signature. / Clathrin adaptor complexes medium chain signature 1. / Clathrin adaptor, mu subunit / Clathrin adaptor, mu subunit, conserved site / Clathrin adaptor complexes medium chain signature 2. / Coatomer/calthrin adaptor appendage, C-terminal subdomain / : / Stimulator of interferon genes protein / Stimulator of interferon genes protein, C-terminal domain superfamily / Transmembrane protein 173 / Adaptor complexes medium subunit family / AP complex, mu/sigma subunit / Clathrin adaptor complex small chain / AP-2 complex subunit mu, C-terminal superfamily / Mu homology domain / Mu homology domain (MHD) profile. / Clathrin adaptor, alpha/beta/gamma-adaptin, appendage, Ig-like subdomain / Adaptin C-terminal domain / Adaptin C-terminal domain / Clathrin/coatomer adaptor, adaptin-like, N-terminal / Adaptin N terminal region / small GTPase Arf family profile. / Clathrin adaptor, appendage, Ig-like subdomain superfamily / Sar1p-like members of the Ras-family of small GTPases / Small GTPase superfamily, ARF/SAR type / ADP-ribosylation factor family / Longin-like domain superfamily / ARF-like small GTPases; ARF, ADP-ribosylation factor / TBP domain superfamily / Armadillo/beta-catenin-like repeats / Armadillo / Rab subfamily of small GTPases / Armadillo-like helical / Small GTP-binding protein domain / Armadillo-type fold / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
AP-1 complex subunit gamma-1 / AP-1 complex subunit mu-1 / ADP-ribosylation factor 1 / AP-1 complex subunit beta-1 / Stimulator of interferon genes protein / AP-1 complex subunit sigma-3
Similarity search - Component
Biological speciesHomo sapiens (human) / Mus musculus (house mouse)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.34 Å
AuthorsXu P / Ablasser A
Funding supportEuropean Union, 1 items
OrganizationGrant numberCountry
European Molecular Biology Organization (EMBO)ALTF-184European Union
CitationJournal: Nature / Year: 2022
Title: Clathrin-associated AP-1 controls termination of STING signalling.
Authors: Ying Liu / Pengbiao Xu / Sophie Rivara / Chong Liu / Jonathan Ricci / Xuefeng Ren / James H Hurley / Andrea Ablasser /
Abstract: Stimulator of interferon genes (STING) functions downstream of cyclic GMP-AMP synthase in DNA sensing or as a direct receptor for bacterial cyclic dinucleotides and small molecules to activate ...Stimulator of interferon genes (STING) functions downstream of cyclic GMP-AMP synthase in DNA sensing or as a direct receptor for bacterial cyclic dinucleotides and small molecules to activate immunity during infection, cancer and immunotherapy. Precise regulation of STING is essential to ensure balanced immune responses and prevent detrimental autoinflammation. After activation, STING, a transmembrane protein, traffics from the endoplasmic reticulum to the Golgi, where its phosphorylation by the protein kinase TBK1 enables signal transduction. The mechanism that ends STING signalling at the Golgi remains unknown. Here we show that adaptor protein complex 1 (AP-1) controls the termination of STING-dependent immune activation. We find that AP-1 sorts phosphorylated STING into clathrin-coated transport vesicles for delivery to the endolysosomal system, where STING is degraded. We identify a highly conserved dileucine motif in the cytosolic C-terminal tail (CTT) of STING that, together with TBK1-dependent CTT phosphorylation, dictates the AP-1 engagement of STING. A cryo-electron microscopy structure of AP-1 in complex with phosphorylated STING explains the enhanced recognition of TBK1-activated STING. We show that suppression of AP-1 exacerbates STING-induced immune responses. Our results reveal a structural mechanism of negative regulation of STING and establish that the initiation of signalling is inextricably associated with its termination to enable transient activation of immunity.
History
DepositionFeb 8, 2022-
Header (metadata) releaseSep 14, 2022-
Map releaseSep 14, 2022-
UpdateNov 9, 2022-
Current statusNov 9, 2022Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_14312.png

Downloads & links

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Map

FileDownload / File: emd_14312.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 0.9 Å
Density
Contour LevelBy AUTHOR: 0.055
Minimum - Maximum-0.18775003 - 0.4890242
Average (Standard dev.)0.0012783447 (±0.013376495)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 270.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_14312_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_14312_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : phospho-STING binding to adaptor protein complex-1

EntireName: phospho-STING binding to adaptor protein complex-1
Components
  • Complex: phospho-STING binding to adaptor protein complex-1
    • Protein or peptide: AP-1 complex subunit beta-1AP-1 transcription factor
    • Protein or peptide: ADP-ribosylation factor 1ARF1
    • Protein or peptide: AP-1 complex subunit gamma-1AP-1 transcription factor
    • Protein or peptide: Stimulator of interferon genes protein
    • Protein or peptide: AP-1 complex subunit mu-1AP-1 transcription factor
    • Protein or peptide: AP-1 complex subunit sigma-3AP-1 transcription factor
  • Ligand: GUANOSINE-5'-TRIPHOSPHATEGuanosine triphosphate
  • Ligand: MAGNESIUM ION

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Supramolecule #1: phospho-STING binding to adaptor protein complex-1

SupramoleculeName: phospho-STING binding to adaptor protein complex-1 / type: complex / Chimera: Yes / ID: 1 / Parent: 0 / Macromolecule list: #1-#6
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)

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Macromolecule #1: AP-1 complex subunit beta-1

MacromoleculeName: AP-1 complex subunit beta-1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 66.008422 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MTDSKYFTTT KKGEIFELKA ELNSDKKEKK KEAVKKVIAS MTVGKDVSAL FPDVVNCMQT DNLELKKLVY LYLMNYAKSQ PDMAIMAVN TFVKDCEDPN PLIRALAVRT MGCIRVDKIT EYLCEPLRKC LKDEDPYVRK TAAVCVAKLH DINAQLVEDQ G FLDTLKDL ...String:
MTDSKYFTTT KKGEIFELKA ELNSDKKEKK KEAVKKVIAS MTVGKDVSAL FPDVVNCMQT DNLELKKLVY LYLMNYAKSQ PDMAIMAVN TFVKDCEDPN PLIRALAVRT MGCIRVDKIT EYLCEPLRKC LKDEDPYVRK TAAVCVAKLH DINAQLVEDQ G FLDTLKDL ISDSNPMVVA NAVAALSEIA ESHPSSNLLD LNPQSINKLL TALNECTEWG QIFILDCLAN YMPKDDREAQ SI CERVTPR LSHANSAVVL SAVKVLMKFM EMLSKDLDYY GTLLKKLAPP LVTLLSAEPE LQYVALRNIN LIVQKRPEIL KHE MKVFFV KYNDPIYVKL EKLDIMIRLA SQANIAQVLA ELREYATEVD VDFVRKAVRA IGRCAIKVEQ SAERCVSTLL DLIQ TKVNY VVQEAIVVIK DIFRKYPNKY ESVIATLCEN LDSLDEPEAR AAMIWIVGEY AERIDNADEL LESFLEGFHD KSTQV QLQL LTAIVKLFLK KPTETQELVQ QVLSLATQDS DNPDLRDRGY IYWRLLSTDP VAAKEVVLAE KPLISEETDL IEPTLL DEL ICYIGTLASV YHKPPSAFVE G

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Macromolecule #2: ADP-ribosylation factor 1

MacromoleculeName: ADP-ribosylation factor 1 / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 18.9366 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString:
EMRILMVGLD AAGKTTILYK LKLGEIVTTI PTIGFNVETV EYKNISFTVW DVGGLDKIRP LWRHYFQNTQ GLIFVVDSND RERVNEARE ELMRMLAEDE LRDAVLLVFA NKQDLPNAMN AAEITDKLGL HSLRHRNWYI QATCATSGDG LYEGLDWLSN Q LRNQK

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Macromolecule #3: AP-1 complex subunit gamma-1

MacromoleculeName: AP-1 complex subunit gamma-1 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 67.399242 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MPAPIRLREL IRTIRTARTQ AEEREMIQKE CAAIRSSFRE EDNTYRCRNV AKLLYMHMLG YPAHFGQLEC LKLIASQKFT DKRIGYLGA MLLLDERQDV HLLMTNCIKN DLNHSTQFVQ GLALCTLGCM GSSEMCRDLA GEVEKLLKTS NSYLRKKAAL C AVHVIRKV ...String:
MPAPIRLREL IRTIRTARTQ AEEREMIQKE CAAIRSSFRE EDNTYRCRNV AKLLYMHMLG YPAHFGQLEC LKLIASQKFT DKRIGYLGA MLLLDERQDV HLLMTNCIKN DLNHSTQFVQ GLALCTLGCM GSSEMCRDLA GEVEKLLKTS NSYLRKKAAL C AVHVIRKV PELMEMFLPA TKNLLNEKNH GVLHTSVVLL TEMCERSPDM LAHFRKLVPQ LVRILKNLIM SGYSPEHDVS GI SDPFLQV RILRLLRILG RNDDDSSEAM NDILAQVATN TETSKNVGNA ILYETVLTIM DIKSESGLRV LAINILGRFL LNN DKNIRY VALTSLLKTV QTDHNAVQRH RSTIVDCLKD LDVSIKRRAM ELSFALVNGN NIRGMMKELL YFLDSCEPEF KADC ASGIF LAAEKYAPSK RWHIDTIMRV LTTAGSYVRD DAVPNLIQLI TNSVEMHAYT VQRLYKAILG DYSQQPLVQV AAWCI GEYG DLLVSGQCEE EEPIQVTEDE VLDILESVLI SNMSTSVTRG YALTAIMKLS TRFTCTVNRI KKVVSIYGSS IDVELQ QRA VEYNALFKKY DHMRSALLER MPVMEKVTTN GP

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Macromolecule #4: Stimulator of interferon genes protein

MacromoleculeName: Stimulator of interferon genes protein / type: protein_or_peptide / ID: 4 / Details: phospho-STING tail / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 1.065068 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString:
QEPELLI(SEP)G

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Macromolecule #5: AP-1 complex subunit mu-1

MacromoleculeName: AP-1 complex subunit mu-1 / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 48.60673 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MSASAVYVLD LKGKVLICRN YRGDVDMSEV EHFMPILMEK EEEGMLSPIL AHGGVRFMWI KHNNLYLVAT SKKNACVSLV FSFLYKVVQ VFSEYFKELE EESIRDNFVI IYELLDELMD FGYPQTTDSK ILQEYITQEG HKLETGAPRP PATVTNAVSW R SEGIKYRK ...String:
MSASAVYVLD LKGKVLICRN YRGDVDMSEV EHFMPILMEK EEEGMLSPIL AHGGVRFMWI KHNNLYLVAT SKKNACVSLV FSFLYKVVQ VFSEYFKELE EESIRDNFVI IYELLDELMD FGYPQTTDSK ILQEYITQEG HKLETGAPRP PATVTNAVSW R SEGIKYRK NEVFLDVIEA VNLLVSANGN VLRSEIVGSI KMRVFLSGMP ELRLGLNDKV LFDNTGRGKS KSVELEDVKF HQ CVRLSRF ENDRTISFIP PDGEFELMSY RLNTHVKPLI WIESVIEKHS HSRIEYMVKA KSQFKRRSTA NNVEIHIPVP NDA DSPKFK TTVGSVKWVP ENSEIVWSVK SFPGGKEYLM RAHFGLPSVE AEDKEGKPPI SVKFEIPYFT TSGIQVRYLK IIEK SGYQA LPWVRYITQN GDYQLRTQ

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Macromolecule #6: AP-1 complex subunit sigma-3

MacromoleculeName: AP-1 complex subunit sigma-3 / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 18.321338 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString:
MIHFILLFSR QGKLRLQKWY ITLPDKERKK ITREIVQIIL SRGHRTSSFV DWKELKLVYK RYASLYFCCA IENQDNELLT LEIVHRYVE LLDKYFGNVC ELDIIFNFEK AYFILDEFII GGEIQETSKK IAVKAIEDSD MLQEVSTVCQ TMGER

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Macromolecule #7: GUANOSINE-5'-TRIPHOSPHATE

MacromoleculeName: GUANOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 7 / Number of copies: 2 / Formula: GTP
Molecular weightTheoretical: 523.18 Da
Chemical component information

ChemComp-GTP:
GUANOSINE-5'-TRIPHOSPHATE / GTP, energy-carrying molecule*YM / Guanosine triphosphate

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Macromolecule #8: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 8 / Number of copies: 2 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration0.8 mg/mL
BufferpH: 7.4
Component:
ConcentrationFormulaName
137.0 mMNaClSodium chloridesodium chloride
2.7 mMKClpotassium chloride
10.0 mMNa2HPO4Sodium phosphate dibasic
1.8 mMKH2PO4Potassium Phosphate, Monobasic

Details: PBS buffer
GridModel: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 1.8 µm / Nominal defocus min: 0.8 µm
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 60.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: OTHER / Details: Ab-initio in cryosparc
Initial angle assignmentType: OTHER / Details: Ab-initio in cryosparc
Final angle assignmentType: OTHER / Details: Cryosparc non-uniform reconstruction
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.34 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 322238
FSC plot (resolution estimation)

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